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At least 91 records · Page 5

The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success

Phylogenetic datasets are now commonly generated using short-read sequencing technologies unhampered by degraded DNA, such as that often extracted from herbarium specimens. The compatibility of these methods with herbarium specimens has precipitated an increase in broad sampling of herbarium specimens for inclusion in phylogenetic studies. Understanding which sample characteristics are predictive of sequencing success can guide researchers in the selection of tissues and specimens most likely to yield good results. Multiple recent studies have considered the relationship between sample characteristics and DNA yield and sequence capture success. Here we report an analysis of the relationship between sample characteristics and sequencing success for nearly 8,000 herbarium specimens. This study, the largest of its kind, is also the first to include a measure of specimen quality (“greenness”) as a predictor of DNA sequencing success. We found that taxonomic group and source herbarium are strong predictors of both DNA yield and sequencing success and that the most important specimen characteristics for predicting success differ for DNA yield and sequencing: greenness was the strongest predictor of DNA yield, and age was the strongest predictor of proportion-on-target reads recovered. Surprisingly, the relationship between age and proportion-on-target reads is the inverse of expectations; older specimens performed slightly better in our capture-based protocols. We also found that DNA yield itself is not a strong predictor of sequencing success. Most literature on DNA sequencing from herbarium specimens considers specimen selection for optimal DNA extraction success, which we find to be an inappropriate metric for predicting success using next-generation sequencing technologies.

54 ENVIRONMENTAL SCIENCES↗

Restoring Soil Fertility on Degraded Lands to Meet Food, Fuel, and Climate Security Needs via Perennialization

A continuously growing pressure to increase food, fiber, and fuel production to meet worldwide demand and achieve zero hunger has put severe pressure on soil resources. Abandoned, degraded, and marginal lands with significant agricultural constraints—many still used for agricultural production—result from inappropriately intensive management, insufficient attention to soil conservation, and climate change. Continued use for agricultural production will often require ever more external inputs such as fertilizers and herbicides, further exacerbating soil degradation and impeding nutrient recycling and retention. Growing evidence suggests that degraded lands have a large potential for restoration, perhaps most effectively via perennial cropping systems that can simultaneously provide additional ecosystem services. Here we synthesize the advantages of and potentials for using perennial vegetation to restore soil fertility on degraded croplands, by summarizing the principal mechanisms underpinning soil carbon stabilization and nitrogen and phosphorus availability and retention. We illustrate restoration potentials with example systems that deliver climate mitigation (cellulosic bioenergy), animal production (intensive rotational grazing), and biodiversity conservation (natural ecological succession). Perennialization has substantial promise for restoring fertility to degraded croplands, helping to meet future food security needs.

54 ENVIRONMENTAL SCIENCES↗

Valuation of Wind Energy Turbines Using Volatility of Wind and Price

The limitedness of the nonrenewable local energy resources in Israel, even in the background of the later gas fields’ findings, continues to force the state to devote various efforts towards ‘green’ energy development. These efforts include installations, both for the solar and for wind energy, thus improving the diversity of energy sources. While the standard discounted cash flow (DCF) method using the net present value (NPV) criterion is extensively adopted to evaluate investments, the standard DCF method is inappropriate for the rapidly changing investment climate and for the managerial flexibility in investment decisions. In recent years, the real options analysis (ROA) technique has been widely applied in many studies for the valuation of renewable energy investment projects. Taking into account the above background, we apply, in this study, the real options analysis approach for the valuation of wind energy turbines and apply it to the analysis of wind energy economic potential in Israel, which is the context of our work. We hypothesize that due to nature of wind energy production uncertainties, the ROA method is better than the alternative. The novelty of this paper includes the following: real world wind statistics of the Merom Golan site in Israel (velocity 3.73 m/s, with a standard deviation of 2.03 m/s), a realistic power generation estimation (power generation of 1205.84 kW with a standard deviation of about 0.5% in annual value which is worth about 1.3 M$ per annum), and an economic model to evaluate the profitability of such a project. We thus discuss the existing challenges of diversifying renewable energy sources in Israel by adding wind installations. Our motivation is to introduce a method which will allow investors and officials to take into account uncertainties when deciding in investing in such wind installations. The outcomes of the paper, which are obtained using the method of Weibull statistics and the Black–Scholes ROA technique, include the result that market price volatility adds to the uncertainties much more than any wind fluctuations, provided that the analysis is integrated over a long enough time.

17 WIND ENERGY↗

PchE Regulation of Escherichia coli O157:H7 Flagella, Controlling the Transition to Host Cell Attachment

Shiga toxins and intimate adhesion controlled by the locus of enterocyte effacement are major enterohemorrhagic Escherichia coli (EHEC) virulence factors. Curli fimbriae also contribute to cell adhesion and are essential biofilm components. The transcriptional regulator PchE represses the expression of curli and their adhesion to HEp-2 cells. Past studies indicate that pchE also represses additional adhesins that contribute to HEp-2 cell attachment. In this study, we tested for pchE regulation of several tissue adhesins and their regulators. Three adhesin-encoding genes (eae, lpfA1, fliC) and four master regulators (csgD, stpA, ler, flhDC) were controlled by pchE. pchE over-expression strongly up-regulated fliC but the marked flagella induction reduced the attachment of O157:H7 clinical isolate PA20 to HEp-2 cells, indicating that flagella were blocking cell attachments rather than functioning as an adhesin. Chemotaxis, motor, structural, and regulatory genes in the flagellar operons were all increased by pchE expression, as was PA20 motility. This study identifies new members in the pchE regulon and shows that pchE stimulates flagellar motility while repressing cell adhesion, likely to support EHEC movement to the intestinal surface early in infection. However, induced or inappropriate pchE-dependent flagellar expression could block cell attachments later during disease progression.

59 BASIC BIOLOGICAL SCIENCES↗

Miniature Beryllium Split-Hopkinson Pressure Bars for Extending the Range of Achievable Strain-Rates

Conventional Split Hopkinson Pressure Bars (SHPB) or “Kolsky” bars are often used for determining the high-rate compressive yield and failure strength of materials. However, for experiments generating very high strain-rates (>10 3 /s) miniaturization of the setup is often required for minimizing the effects of elastic wave dispersion in order to enable the inference of decreasingly short loading events from the data. Miniature aluminum and steel bars are often sufficient for meeting these requirements. However, for high enough strain-rates, miniaturization of steel or aluminum Kolsky bars may require prohibitively small diameter bars and test specimens that could become inappropriate for inferring representative properties of materials with large grain size relative to the test specimen size. The use of a beryllium Kolsky bar setup is expected to enable high rates to be accessible with larger diameter bars/specimen combinations due to the inherent physical properties of beryllium, which are expected to minimize the effects of elastic wave dispersion. For this reason, a series of beryllium Kolsky bars have been developed, and, in this paper, the dispersion characteristics of these bars are measured and compare the data with those of similarly sized 7075-T6 aluminum and C350 maraging steel. The results, which agree well with the theory, show no appreciable frequency dependence of the elastic wavespeed in the data from the beryllium bars, demonstrating its advantage over aluminum and steel in application to Kolsky bars.

36 MATERIALS SCIENCE↗

Cluster-dynamics-based parameterization for sulfuric acid–dimethylamine nucleation: comparison and selection through box and three-dimensional modeling

Clustering of gaseous sulfuric acid (SA) enhanced by dimethylamine (DMA) is a major mechanism for new particle formation (NPF) in polluted atmospheres. However, uncertainty remains regarding the SA–DMA nucleation parameterization that reasonably represents cluster dynamics and is applicable across various atmospheric conditions. This uncertainty hinders accurate three-dimensional (3-D) modeling of NPF and the subsequent assessment of its environmental and climatic impacts. Here we extensively compare different cluster-dynamics-based parameterizations for SA–DMA nucleation and identify the most reliable one through a combination of box model simulations, 3-D modeling, and in situ observations. Results show that the parameterization derived from Atmospheric Cluster Dynamic Code (ACDC) simulations, incorporating the latest theoretical insights (DLPNO-CCSD(T)/aug-cc-pVTZ//ωB97X-D/6-311++G(3df,3pd) level of theory) and adequate representation of cluster dynamics, exhibits dependable performance in 3-D NPF simulation for both winter and summer conditions in Beijing and shows promise for application in diverse atmospheric conditions. Another ACDC-derived parameterization, replacing the level of theory with RI-CC2/aug-cc-pV(T+d)Z//M06-2X/6–311++G(3df,3pd), also performs well in NPF modeling at relatively low temperatures around 280 K but exhibits limitations at higher temperatures due to inappropriate representation of SA–DMA cluster thermodynamics. Additionally, a previously reported parameterization incorporating simplifications is applicable for simulating NPF in polluted atmospheres but tends to overestimate particle formation rates under conditions of elevated temperature (>∼300 K) and low-condensation sink (<∼3×10 -3 s −1 ). Our findings highlight the applicability of the new ACDC-derived parameterization, which couples the latest SA–DMA nucleation theory and holistic cluster dynamics, in 3-D NPF modeling. The ACDC-derived parameterization framework provides a valuable reference for developing parameterizations for other nucleation systems.

Shen, Jiewen↗

Definition and application of longitudinal stability derivatives for elastic airplanes

A set of longitudinal stability derivatives for elastic airplanes is defined from fundamental principles allowing perturbations in forward speed. Application of these derivatives to longitudinal stability analysis by use of approximate expressions for static stability and control parameters as well as the dynamic equations of motion is illustrated. One commonly used alternative formulation for elastic airplanes is shown to yield significant inaccuracies because of inappropriate interpretation of inertial effects.

Kemp, W. B., Jr.↗

The effect of changing gravity and weightlessness of vasopressin control systems

An immunoassay to determine the effects of changing gravity and weightlessness on vasopressin control system is discussed. Seven extracts from persons known to have inappropriate ADH syndrome secondary to pulmonary oat cell cancer were examined. The extracts had previously been subject to bioassay in rats. The intent of the examination was to determine if the vasopressin content could be confirmed immunologically. The results compared favorably with the values obtained by biological assay.

Moran, W. H.↗

Workshop on dimensional analysis for design, development, and research executives

The proceedings of a conference of research and development executives are presented. The purpose of the meeting was to develop an understanding of the conditions which are appropriate for the use of certain general management tools and those conditions which render these tools inappropriate. The verbatim statements of the participants are included to show the direction taken initially by the conference. Formal presentations of management techniques for research and development are developed.

Goodman, R. A.↗

A survey of local interstellar hydrogen from OAO-2 observations of Lyman alpha absorption.

A far UV spectrometer aboard OAO-2 observed the wavelength region near 1216 A for 69 stars of spectral type B2 or earlier. From the strength of the observed interstellar L-alpha absorption, column densities of atomic hydrogen were derived over distances averaging 300 pc away from the sun. Measurements of the equivalent widths of this absorption were found to be inappropriate for deducing column densities because of the blending of nearby strong stellar lines by the 12 A wide instrumental profile of the OAO. Instead, the OAO data were compared with synthetic UV spectra, originally derived from earlier higher-resolution rocket observations, which were computer processed to simulate the effects of absorption by different amounts of hydrogen followed by the instrumental blending.

Savage, B. D.↗

Theoretical model of vertical distributions of CO and CH4 in the mesosphere and upper stratosphere.

Carbon compounds (CO and CO2) and methane are added to an existing computer program (Shimazaki and Laird, 1970, 1972), which calculates diurnal variations in density distributions of pure oxygen compounds, hydrogen compounds, and nitrogen compounds. For the present model calculations, the original program was modified to calculate the steady-state profiles for all constituents, and then these solutions were used as the initial condition for solving the time-dependent equations. The effects of chemical reactions and vertical eddy diffusion transport on the CH4 and CO concentrations above 40 km, where one-dimensional treatment may not be too inappropriate, are discussed. Some of the 15 constituents included in the computer program interact with CO and CH4 chemically, and CH4 is more sensitive to the eddy diffusion coefficient than any other constituent. Therefore it is easier to determine the most appropriate profile of the eddy diffusion coefficient by comparing the model profile with the observations for CH4.

Shimazaki, T.↗

Evaluation of polyimide/glass fiber composites for construction of light weight pressure vessels for cryogenic propellants

The application of polyimide resin as a matrix for glass filament-wound thin metal-lined pressure vessels was studied over a temperature range of (minus) 320 to 600 F. Keramid 601 polyimide was found to perform quite well over the entire range of temperature. Hoop stress values of 425 ksi were determined at 75 F which is equivalent to epoxy resin in similar structures. At -320 and 600 F, 125 and 80% of this strength was retained. Thermal ageing at 500 F for up to 50 hours was studied with severe reduction in strength, but there is evidence that this reduction could be improved. Another polyimide resin studied was P10PA which was found to have processing characteristics inappropriate for filament-winding. NOL ring tensile and shear data was determined from both resins with S-glass. Pressure vessel design, fabrication and test procedures are described in detail.

Petker, I.↗

Human Factors Research Problems in Electronic Voice Warning System Design

The speech messages issued by voice warning systems must be carefully designed in accordance with general principles of human decision making processes, human speech comprehension, and the conditions in which the warnings can occur. The operator's effectiveness must not be degraded by messages that are either inappropriate or difficult to comprehend. Important experimental variables include message content, linguistic redundancy, signal/noise ratio, interference with concurrent tasks, and listener expectations generated by the pragmatic or real world context in which the messages are presented.

C A Simpson↗

A new computer approach to mixed feature classification for forestry application

A computer approach for mapping mixed forest features (i.e., types, classes) from computer classification maps is discussed. Mixed features such as mixed softwood/hardwood stands are treated as admixtures of softwood and hardwood areas. Large-area mixed features are identified and small-area features neglected when the nominal size of a mixed feature can be specified. The computer program merges small isolated areas into surrounding areas by the iterative manipulation of the postprocessing algorithm that eliminates small connected sets. For a forestry application, computer-classified LANDSAT multispectral scanner data of the Sam Houston National Forest were used to demonstrate the proposed approach. The technique was successful in cleaning the salt-and-pepper appearance of multiclass classification maps and in mapping admixtures of softwood areas and hardwood areas. However, the computer-mapped mixed areas matched very poorly with the ground truth because of inadequate resolution and inappropriate definition of mixed features.

Kan, E. P.↗

Ultrasonic measurement of stress in 2219-T87 aluminum plate

The basic relationship of ultrasonic signal velocity to directional subsurface stress is reviewed. Inappropriateness of dependency on a single correlative value of constant for a three dimensional stress field in metallic materials is discussed. Implementation of conventional ultrasonic nondestructive testing capabilities integrated to provide a composite technique for the measurement of orthogonal stress components is described, and the procedures for performing the preparatory calibration and subsequent stress field measurements are presented. In conclusion, the prime effect of stress on ultrasonic signal velocity occurs only in the direction of material excitation or particle motion.

Clotfelter, W. N.↗

Ocean color spectra measured off the Oregon coast - Characteristic vectors

The ocean color spectrum is defined as the ratio of the spectrum of light upwelled from the sea to the spectrum of light incident on the sea surface. Ocean color spectra, observed from an airplane flown over waters off Oregon, are analyzed. The original spectra are resolved into fifty-five wavelength bands, each 5 nm wide. The shapes of these spectra are parameterized by, and shown to be accurately recoverable from, their first four principal components. These components are the scalar projections of each spectrum on the first four characteristic vectors of the sample covariance matrix. Regression equations are found with which phytoplankton pigment concentration and water transparency may be estimated as linear functions of the principal components. Pigment concentration estimates thus obtained are imprecise. The poor fit is at least partly due to the inappropriateness of the linear regression model and the neglect of other optically important substances typically present in sea water.

Mueller, J. L.↗

Analysis of bilinear noise models in circuits and devices

There are a number of applications in which linear noise models are inappropriate. In the paper, the use of bilinear noise models in circuits and devices is considered. Several physical problems are studied in this framework. These include circuits involving varying parameters (such as variable resistance circuits constructed using field-effect transistors), the effect of switching jitter on sampled data system performance and communication systems involving voltage-controlled oscillators and phase-lock loops. In addition, several types of analytical techniques for stochastic bilinear systems are considered. Specifically, the moment equations of Brockett for bilinear systems driven by white noise are discussed, and closed-form expressions for certain bilinear systems (those that evolve an Abelian or solvable Lie groups) driven by white or colored noise are derived. In addition, an approximate statistical technique involving the use of harmonic expansions is described.

Willsky, A. S.↗